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On 4/27/2011 9:40 PM, Lipi Thukral wrote:
<blockquote
cite="mid:BANLkTi=YqcaLGR+L5+-v4FBEUub3+3nLRA@mail.gmail.com"
type="cite">
<div style="border-collapse: collapse; font-family:
arial,sans-serif; font-size: 13px;"><span
style="border-collapse: collapse; font-family:
arial,sans-serif; font-size: 13px;">Dear David,</span></div>
<div style="border-collapse: collapse; font-family:
arial,sans-serif; font-size: 13px;">
<span style="border-collapse: collapse; font-family:
arial,sans-serif; font-size: 13px;">Dear Justin,</span></div>
<div style="border-collapse: collapse; font-family:
arial,sans-serif; font-size: 13px;"><span
style="border-collapse: collapse; font-family:
arial,sans-serif; font-size: 13px;"><br>
</span></div>
<div style="border-collapse: collapse; font-family:
arial,sans-serif; font-size: 13px;"><span
style="border-collapse: collapse; font-family:
arial,sans-serif; font-size: 13px;">I have now installed the
latest version of Gromacs 4.5.4. The problem still persists. </span></div>
<div style="border-collapse: collapse; font-family:
arial,sans-serif; font-size: 13px;">The two files to concatenate
do not have exactly the same timeframes. However they do have
something like the following:</div>
<div style="border-collapse: collapse; font-family:
arial,sans-serif; font-size: 13px;">
<br>
</div>
<div><font face="arial, sans-serif"><span style="border-collapse:
collapse;">File 1: 2091000.0000000</span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:
collapse;">File 2: 2090170.0000000</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span
class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span
class="Apple-style-span" style="border-collapse: collapse;">May
be I don't understand but its clear that the two files do
not have the same time-frames so why is trjcat skipping the
frames?</span></font></div>
</blockquote>
<br>
trjcat is intended to con*cat*enate files that are parts of the same
logical trajectory. If there's overlapping time frames, then you'll
have to make sensible decisions yourself. It sounds like your first
frame in the second trajectory occurs at a time that is in the range
covered by the second trajectory. This doesn't make sense to trjcat,
and apparently its defaults aren't what you (think you) want it to
do. Read trjcat -h and choose wisely.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTi=YqcaLGR+L5+-v4FBEUub3+3nLRA@mail.gmail.com"
type="cite">
<div><font class="Apple-style-span" face="arial, sans-serif"><span
class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span
class="Apple-style-span" style="border-collapse: collapse;">Regards,</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span
class="Apple-style-span" style="border-collapse: collapse;">Lipi</span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:
collapse;"><br>
</span></font></div>
<div style="border-collapse: collapse; font-family:
arial,sans-serif; font-size: 13px;"><br>
</div>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">On 4/27/2011 3:51 PM, Lipi Thukral wrote:</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> Hi Justin,</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> I am using Gromacs 4.5 beta-2.</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> gmxcheck with file 1 and file 2 tells me
exactly the number of frames</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> I specified.</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> gmxcheck -f File1.xtc</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> Frames: 2175</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> gmxcheck -f File2.xtc</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> Frames: 1232</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> While after concatenating, it skips the frames
and the combined</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> trajectory results in 1266 frames.</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> Do you attribute this to Gromacs4.5beta2
version? Is there a possible</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> bug in that version for trjcat?</span></font><br>
<br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">Maybe - but it's not worth finding out whether a
bug existed then.</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">There's no value in trouble-shooting a beta version
that is known to</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">have other problems. Get the latest GROMACS version
and install and use</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">it. If you can demonstrate a problem there, now
people will be much more</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">interested in addressing the issue.</span></font><br>
<br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">Mark</span></font><br>
<br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> Regards,</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> Lipi</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> Lipi Thukral wrote:</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> > Dear gmx-users,</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> ></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> > I intended to concantanate two
trajectories with no similar time frames</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> > i.e., both files have distinct time
frames. But once I combine the files</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> > many time frames are skipped, details are
as follows:</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> ></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> > File 1 has 2175 frames</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> > File 2 has 1232 frames</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> ></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> What does gmxcheck tell you about each of
these files?</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> > I used the following command to
concatenate:</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> ></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> > trjcat -f File1.xtc File2.xtc -o
CombinedFile3.xtc</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> ></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> > Now I obtained in total 1266 frames
instead of 3407 frames as expected.</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> > When I compared the CombinedFile3 with
both File 1 and File 2, I found</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> > that it has somehow taken the first 34
frames from File 1 and rest of</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> > the frames belongs to File 2 i.e., the
last file.</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> ></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> > I am unable to understand why trjcat
skips the frames inspite of no</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> > similarity. I am using 4.5-beta version
of Gromacs. I am also open to</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> > sharing the files, should that be needed.</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> ></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> There have been numerous beta versions over
the last few years, none</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> of which</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> should necessarily be considered stable.
Which beta are you using</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> exactly?</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> -Justin</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> > Any possible explanation as to why I am
obtaining the combined</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> > trajectory with skipping frames, would be
really helpful.</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> ></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> > Many Thanks,</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> > Lipi</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> ></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> --</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> ==============================</span></font><font
face="arial, sans-serif"><span style="border-collapse:
collapse;">==========</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> Justin A. Lemkul</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> Ph.D. Candidate</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> ICTAS Doctoral Scholar</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> MILES-IGERT Trainee</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> Department of Biochemistry</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> Virginia Tech</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> Blacksburg, VA</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> jalemkul[at]</span></font><a
moz-do-not-send="true" href="http://vt.edu/" style="color:
rgb(0, 101, 204); border-collapse: collapse; font-family:
arial,sans-serif; font-size: 13px;" target="_blank">vt.edu</a><font
face="arial, sans-serif"><span style="border-collapse:
collapse;"> <</span></font><a moz-do-not-send="true"
href="http://vt.edu/" style="color: rgb(0, 101, 204);
border-collapse: collapse; font-family: arial,sans-serif;
font-size: 13px;" target="_blank">http://vt.edu/</a><font
face="arial, sans-serif"><span style="border-collapse:
collapse;">> | (540) 231-9080</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> </span></font><a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
style="color: rgb(0, 101, 204); border-collapse: collapse;
font-family: arial,sans-serif; font-size: 13px;" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:
collapse;">> ==============================</span></font><font
face="arial, sans-serif"><span style="border-collapse:
collapse;">==========</span></font>
</blockquote>
<br>
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